Transactions on Computational Systems Biology II

Guillaume Blin, Guillaume Fertin (auth.), Corrado Priami, Alexander Zelikovsky (eds.)3540294015, 9783540294016

The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena.

This second volume of the Transactions on Computational Systems Biology is devoted to considerably extended versions of selected papers presented at the International Workshop on Bioinformatics Research and Applications (IWBRA 2005), part of the International Conference on Computational Science (ICCS 2005), which took place at Emory University, Atlanta, Georgia, USA, in May 2005.

The ten papers selected for the special issue cover a wide range of bioinformatics research such as problems in RNA structure prediction, coding schemes and structural alphabets for protein structure prediction, novel techniques for efficient gene transfer in phylogenetic networks, practical algorithms minimizing recombinations in pedigree phasing, parallel implementation in Open MP for finding the corresponding shortest edit distance between two signed gene permutations, and bioinformatics problems in DNA microarrays.

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Table of contents :
Front Matter….Pages –
What Makes the Arc-Preserving Subsequence Problem Hard?….Pages 1-36
Profiling and Searching for RNA Pseudoknot Structures in Genomes….Pages 37-47
A Class of New Kernels Based on High-Scored Pairs of k -Peptides for SVMs and Its Application for Prediction of Protein Subcellular Localization….Pages 48-58
A Protein Structural Alphabet and Its Substitution Matrix CLESUM….Pages 59-67
KXtractor: An Effective Biomedical Information Extraction Technique Based on Mixture Hidden Markov Models….Pages 68-81
Phylogenetic Networks: Properties and Relationship to Trees and Clusters….Pages 82-99
Minimum Parent-Offspring Recombination Haplotype Inference in Pedigrees….Pages 100-112
Calculating Genomic Distances in Parallel Using OpenMP….Pages 113-123
Improved Tag Set Design and Multiplexing Algorithms for Universal Arrays….Pages 124-137
Virtual Gene: Using Correlations Between Genes to Select Informative Genes on Microarray Datasets….Pages 138-152
Back Matter….Pages –